# Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

## Documentation for package ‘aroma.core’ version 3.3.2

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

aroma.core-package | Package aroma.core
AbstractCNData | The AbstractCNData class
AbstractPSCNData | The AbstractPSCNData class
aroma.core | Package aroma.core
AromaCellCpgFile | A binary file holding local CpG density for each cell (probe/feature)
AromaCellPositionFile | A binary file holding chromosome/position for each cell
AromaCellTabularBinaryFile | The AromaCellTabularBinaryFile class
AromaGenomeTextFile | The AromaGenomeTextFile class
AromaMicroarrayDataFile | The abstract AromaMicroarrayDataFile class
AromaMicroarrayDataSet | The AromaMicroarrayDataSet class
AromaMicroarrayDataSetTuple | The AromaMicroarrayDataSetTuple class
AromaMicroarrayTabularBinaryFile | The AromaMicroarrayTabularBinaryFile class
AromaPlatform | The AromaPlatform class
AromaPlatformInterface | The AromaPlatformInterface class
AromaRepository | The AromaRepository class
AromaTabularBinaryFile | The AromaTabularBinaryFile class
AromaTabularBinarySet | The AromaTabularBinarySet class
AromaTransform | The AromaTransform class
AromaUnitCallFile | The AromaUnitCallFile class
AromaUnitCallSet | The AromaUnitCallSet class
AromaUnitFracBCnBinaryFile | The AromaUnitFracBCnBinaryFile class
AromaUnitFracBCnBinarySet | The AromaUnitFracBCnBinarySet class
AromaUnitGenotypeCallFile | The AromaUnitGenotypeCallFile class
AromaUnitGenotypeCallSet | The AromaUnitGenotypeCallSet class
AromaUnitPscnBinaryFile | The AromaUnitPscnBinaryFile class
AromaUnitPscnBinarySet | The AromaUnitPscnBinarySet class
AromaUnitSignalBinaryFile | The AromaUnitSignalBinaryFile class
AromaUnitSignalBinarySet | The AromaUnitSignalBinarySet class
AromaUnitTabularBinaryFile | The AromaUnitTabularBinaryFile class
AromaUnitTotalCnBinaryFile | The AromaUnitTotalCnBinaryFile class
AromaUnitTotalCnBinarySet | The AromaUnitTotalCnBinarySet class
AromaUnitTypesFile | The AromaUnitTypesFile class
BinnedScatter | The BinnedScatter class
binnedSmoothing | Binned smoothing of a matrix column by column
binnedSmoothing.numeric | Binned smoothing of a matrix column by column
CbsModel | The CbsModel class
ChromosomalModel | The ChromosomalModel class
ChromosomeExplorer | The ChromosomeExplorer class
colBinnedSmoothing | Binned smoothing of a matrix column by column
colBinnedSmoothing.matrix | Binned smoothing of a matrix column by column
colKernelSmoothing | Kernel smoothing of a matrix column by column
colKernelSmoothing.matrix | Kernel smoothing of a matrix column by column
CopyNumberChromosomalModel | The CopyNumberChromosomalModel class
CopyNumberSegmentationModel | The CopyNumberSegmentationModel class
doCBS | Performs Circular Binary Segmentation (CBS) on a data set
doCBS.character | Performs Circular Binary Segmentation (CBS) on a data set
doCBS.CopyNumberDataSet | Performs Circular Binary Segmentation (CBS) on a data set
doCBS.CopyNumberDataSetTuple | Performs Circular Binary Segmentation (CBS) on a data set
doCBS.default | Performs Circular Binary Segmentation (CBS) on a data set
Explorer | The Explorer class
GladModel | The GladModel class
HaarSegModel | The HaarSegModel class
kernelSmoothing | Kernel smoothing of a matrix column by column
kernelSmoothing.numeric | Kernel smoothing of a matrix column by column
NonPairedPSCNData | The NonPairedPSCNData class
PairedPSCNData | The PairedPSCNData class
ParametersInterface | The ParametersInterface class interface
RawAlleleBFractions | The RawAlleleBFractions class
RawCopyNumberModel | The RawCopyNumberModel class
RawCopyNumbers | The RawCopyNumbers class
RawGenomicSignals | The RawGenomicSignals class
RawMirroredAlleleBFractions | The RawMirroredAlleleBFractions class
RawSequenceReads | The RawSequenceReads class
SegmentedAlleleBFractions | The SegmentedAlleleBFractions class
SegmentedCopyNumbers | The SegmentedCopyNumbers class
SegmentedGenomicSignalsInterface | The SegmentedGenomicSignalsInterface class interface
UnitAnnotationDataFile | The UnitAnnotationDataFile interface class
UnitNamesFile | The UnitNamesFile interface class
UnitTypesFile | The UnitTypesFile interface class